let index     ~reference_build     ~(run_with : Machine.t) =   let open KEDSL in   let reference_fasta =     Machine.get_reference_genome run_with reference_build     |> Reference_genome.fasta in   let star_tool = Machine.get_tool run_with Machine.Tool.Default.star in   let name =     sprintf "star-index-%s" (Filename.basename reference_fasta#product#path) in   let reference_annotations =     Machine.get_reference_genome run_with reference_build |> Reference_genome.gtf_exn in   let reference_dir = (Filename.dirname reference_fasta#product#path) in   let result_dir = sprintf "%s/star-index/" reference_dir in   let suffix_array_result = result_dir // "SA" in   let processors = Machine.max_processors run_with in   workflow_node ~name     (single_file ~host:(Machine.(as_host run_with)) suffix_array_result)     ~edges:[       on_failure_activate (Remove.directory ~run_with result_dir);       depends_on reference_fasta;       depends_on Machine.Tool.(ensure star_tool);     ]     ~tags:[Target_tags.aligner]     ~make:(Machine.run_big_program run_with ~processors ~name              ~self_ids:["star"; "index"]              Program.(                Machine.Tool.(init star_tool)                && shf "mkdir %s" result_dir                && shf "STAR --runMode genomeGenerate --genomeDir %s --genomeFastaFiles %s --sjdbGTFfile %s --runThreadN %d"                  result_dir                  (Filename.quote reference_fasta#product#path)                  (Filename.quote reference_annotations#product#path)                  processors              ))